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PLoS Genetics

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https://www.readbyqxmd.com/read/28234902/kinetics-of-large-scale-chromosomal-movement-during-asymmetric-cell-division-in-escherichia-coli
#1
Jaana Männik, Matthew W Bailey, Jordan C O'Neill, Jaan Männik
Coordination between cell division and chromosome replication is essential for a cell to produce viable progeny. In the commonly accepted view, Escherichia coli realize this coordination via the accurate positioning of its cell division apparatus relative to the nucleoids. However, E. coli lacking proper positioning of its cell division planes can still successfully propagate. Here, we characterize how these cells partition their chromosomes into daughters during such asymmetric divisions. Using quantitative time-lapse imaging, we show that DNA translocase, FtsK, can pump as much as 80% (3...
February 24, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28234896/suppressor-of-rid1-sid1-shares-common-targets-with-rid1-on-florigen-genes-to-initiate-floral-transition-in-rice
#2
Li Deng, Lingmei Li, Shuo Zhang, Jianqiang Shen, Shaobo Li, Sifan Hu, Qiang Peng, Jinghua Xiao, Changyin Wu
The transition from vegetative to reproductive growth is a critical process in the life cycle of higher plants. Previously, we cloned Rice Indeterminate 1 (RID1), which acts as the master switch for the transition from the vegetative to reproductive phase in rice. Although the photoperiod pathway of RID1 inducing expression of the florigen genes Hd3a and RFT1 via Ehd1 has been established, the alternative pathways for the essential flowering transition need to be further examined. Here, we identified a Suppressor of rid1 (SID1), which rescues the never-flowering phenotype of rid1...
February 24, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28234895/a-new-link-between-transcriptional-initiation-and-pre-mrna-splicing-the-rna-binding-histone-variant-h2a-b
#3
Tatiana A Soboleva, Brian J Parker, Maxim Nekrasov, Gene Hart-Smith, Ying Jin Tay, Wei-Quan Tng, Marc Wilkins, Daniel Ryan, David J Tremethick
The replacement of histone H2A with its variant forms is critical for regulating all aspects of genome organisation and function. The histone variant H2A.B appeared late in evolution and is most highly expressed in the testis followed by the brain in mammals. This raises the question of what new function(s) H2A.B might impart to chromatin in these important tissues. We have immunopurified the mouse orthologue of H2A.B, H2A.B.3, from testis chromatin and found this variant to be associated with RNA processing factors and RNA Polymerase (Pol) II...
February 24, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28231279/lysine-acetyltransferase-nua4-and-acetyl-coa-regulate-glucose-deprived-stress-granule-formation-in-saccharomyces-cerevisiae
#4
Meaghen Rollins, Sylvain Huard, Alan Morettin, Jennifer Takuski, Trang Thuy Pham, Morgan D Fullerton, Jocelyn Côté, Kristin Baetz
Eukaryotic cells form stress granules under a variety of stresses, however the signaling pathways regulating their formation remain largely unknown. We have determined that the Saccharomyces cerevisiae lysine acetyltransferase complex NuA4 is required for stress granule formation upon glucose deprivation but not heat stress. Further, the Tip60 complex, the human homolog of the NuA4 complex, is required for stress granule formation in cancer cell lines. Surprisingly, the impact of NuA4 on glucose-deprived stress granule formation is partially mediated through regulation of acetyl-CoA levels, which are elevated in NuA4 mutants...
February 23, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28231245/signalling-crosstalk-at-the-leading-edge-controls-tissue-closure-dynamics-in-the-drosophila-embryo
#5
Raphaël Rousset, Fabrice Carballès, Nadège Parassol, Sébastien Schaub, Delphine Cérézo, Stéphane Noselli
Tissue morphogenesis relies on proper differentiation of morphogenetic domains, adopting specific cell behaviours. Yet, how signalling pathways interact to determine and coordinate these domains remains poorly understood. Dorsal closure (DC) of the Drosophila embryo represents a powerful model to study epithelial cell sheet sealing. In this process, JNK (JUN N-terminal Kinase) signalling controls leading edge (LE) differentiation generating local forces and cell shape changes essential for DC. The LE represents a key morphogenetic domain in which, in addition to JNK, a number of signalling pathways converges and interacts (anterior/posterior -AP- determination; segmentation genes, such as Wnt/Wingless; TGFβ/Decapentaplegic)...
February 23, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28222102/anln-truncation-causes-a-familial-fatal-acute-respiratory-distress-syndrome-in-dalmatian-dogs
#6
Saila Holopainen, Marjo K Hytönen, Pernilla Syrjä, Meharji Arumilli, Anna-Kaisa Järvinen, Minna Rajamäki, Hannes Lohi
Acute respiratory distress syndrome (ARDS) is the leading cause of death in critical care medicine. The syndrome is typified by an exaggerated inflammatory response within the lungs. ARDS has been reported in many species, including dogs. We have previously reported a fatal familial juvenile respiratory disease accompanied by occasional unilateral renal aplasia and hydrocephalus, in Dalmatian dogs. The condition with a suggested recessive mode of inheritance resembles acute exacerbation of usual interstitial pneumonia in man...
February 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28222097/a-genome-wide-association-study-identifies-a-lncrna-as-risk-factor-for-pathological-inflammatory-responses-in-leprosy
#7
Vinicius M Fava, Jeremy Manry, Aurélie Cobat, Marianna Orlova, Nguyen Van Thuc, Milton O Moraes, Carolinne Sales-Marques, Mariane M A Stefani, Ana Carla P Latini, Andrea F Belone, Vu Hong Thai, Laurent Abel, Alexandre Alcaïs, Erwin Schurr
Leprosy Type-1 Reactions (T1Rs) are pathological inflammatory responses that afflict a sub-group of leprosy patients and result in peripheral nerve damage. Here, we employed a family-based GWAS in 221 families with 229 T1R-affect offspring with stepwise replication to identify risk factors for T1R. We discovered, replicated and validated T1R-specific associations with SNPs located in chromosome region 10p21.2. Combined analysis across the three independent samples resulted in strong evidence of association of rs1875147 with T1R (p = 4...
February 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28222093/active-zone-proteins-are-transported-via-distinct-mechanisms-regulated-by-par-1-kinase
#8
Kara R Barber, Julia Tanquary, Keegan Bush, Amanda Shaw, Michael Woodson, Michael Sherman, Yogesh P Wairkar
Disruption of synapses underlies a plethora of neurodevelopmental and neurodegenerative disease. Presynaptic specialization called the active zone plays a critical role in the communication with postsynaptic neuron. While the role of many proteins at the active zones in synaptic communication is relatively well studied, very little is known about how these proteins are transported to the synapses. For example, are there distinct mechanisms for the transport of active zone components or are they all transported in the same transport vesicle? Is active zone protein transport regulated? In this report we show that overexpression of Par-1/MARK kinase, a protein whose misregulation has been implicated in Autism spectrum disorders (ASDs) and neurodegenerative disorders, lead to a specific block in the transport of an active zone protein component- Bruchpilot at Drosophila neuromuscular junctions...
February 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28222092/the-genetic-basis-of-resistance-and-matching-allele-interactions-of-a-host-parasite-system-the-daphnia-magna-pasteuria-ramosa-model
#9
Gilberto Bento, Jarkko Routtu, Peter D Fields, Yann Bourgeois, Louis Du Pasquier, Dieter Ebert
Negative frequency-dependent selection (NFDS) is an evolutionary mechanism suggested to govern host-parasite coevolution and the maintenance of genetic diversity at host resistance loci, such as the vertebrate MHC and R-genes in plants. Matching-allele interactions of hosts and parasites that prevent the emergence of host and parasite genotypes that are universally resistant and infective are a genetic mechanism predicted to underpin NFDS. The underlying genetics of matching-allele interactions are unknown even in host-parasite systems with empirical support for coevolution by NFDS, as is the case for the planktonic crustacean Daphnia magna and the bacterial pathogen Pasteuria ramosa...
February 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28212378/sequencing-the-extrachromosomal-circular-mobilome-reveals-retrotransposon-activity-in-plants
#10
Sophie Lanciano, Marie-Christine Carpentier, Christel Llauro, Edouard Jobet, Dagmara Robakowska-Hyzorek, Eric Lasserre, Alain Ghesquière, Olivier Panaud, Marie Mirouze
Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants...
February 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28212376/the-legionella-pneumophila-genome-evolved-to-accommodate-multiple-regulatory-mechanisms-controlled-by-the-csra-system
#11
Tobias Sahr, Christophe Rusniok, Francis Impens, Giulia Oliva, Odile Sismeiro, Jean-Yves Coppée, Carmen Buchrieser
The carbon storage regulator protein CsrA regulates cellular processes post-transcriptionally by binding to target-RNAs altering translation efficiency and/or their stability. Here we identified and analyzed the direct targets of CsrA in the human pathogen Legionella pneumophila. Genome wide transcriptome, proteome and RNA-Co-immunoprecipitaion followed by deep sequencing of a wild type and a csrA mutant strain identified 479 RNAs with potential CsrA interaction sites located in the untranslated and/or coding regions of mRNAs or of known non-coding sRNAs...
February 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28212375/epilepsy-associated-gene-nedd4-2-mediates-neuronal-activity-and-seizure-susceptibility-through-ampa-receptors
#12
Jiuhe Zhu, Kwan Young Lee, Kathryn A Jewett, Heng-Ye Man, Hee Jung Chung, Nien-Pei Tsai
The neural precursor cell expressed developmentally down-regulated gene 4-2, Nedd4-2, is an epilepsy-associated gene with at least three missense mutations identified in epileptic patients. Nedd4-2 encodes a ubiquitin E3 ligase that has high affinity toward binding and ubiquitinating membrane proteins. It is currently unknown how Nedd4-2 mediates neuronal circuit activity and how its dysfunction leads to seizures or epilepsies. In this study, we provide evidence to show that Nedd4-2 mediates neuronal activity and seizure susceptibility through ubiquitination of GluA1 subunit of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor, (AMPAR)...
February 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28207814/jmjd-5-kdm8-regulates-h3k36me2-and-is-required-for-late-steps-of-homologous-recombination-and-genome-integrity
#13
Pier Giorgio Amendola, Nico Zaghet, João J Ramalho, Jens Vilstrup Johansen, Mike Boxem, Anna Elisabetta Salcini
The eukaryotic genome is organized in a three-dimensional structure called chromatin, constituted by DNA and associated proteins, the majority of which are histones. Post-translational modifications of histone proteins greatly influence chromatin structure and regulate many DNA-based biological processes. Methylation of lysine 36 of histone 3 (H3K36) is a post-translational modification functionally relevant during early steps of DNA damage repair. Here, we show that the JMJD-5 regulates H3K36 di-methylation and it is required at late stages of double strand break repair mediated by homologous recombination...
February 16, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28207750/functional-exploration-of-the-ift-a-complex-in-intraflagellar-transport-and-ciliogenesis
#14
Bing Zhu, Xin Zhu, Limei Wang, Yinwen Liang, Qianqian Feng, Junmin Pan
Intraflagellar transport (IFT) particles or trains are composed of IFT-A and IFT-B complexes. To assess the working mechanism of the IFT-A complex in IFT and ciliogenesis, we have analyzed ift43 mutants of Chlamydomnonas in conjunction with mutants of the other IFT-A subunits. An ift43 null mutant or a mutant with a partial deletion of the IFT43 conserved domain has no or short flagella. The mutants accumulate not only IFT-B but also IFT-Ain the short flagella, which is in contrast to an ift140 null mutant...
February 16, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28207748/nucleotide-pools-dictate-the-identity-and-frequency-of-ribonucleotide-incorporation-in-mitochondrial-dna
#15
Anna-Karin Berglund, Clara Navarrete, Martin K M Engqvist, Emily Hoberg, Zsolt Szilagyi, Robert W Taylor, Claes M Gustafsson, Maria Falkenberg, Anders R Clausen
Previous work has demonstrated the presence of ribonucleotides in human mitochondrial DNA (mtDNA) and in the present study we use a genome-wide approach to precisely map the location of these. We find that ribonucleotides are distributed evenly between the heavy- and light-strand of mtDNA. The relative levels of incorporated ribonucleotides reflect that DNA polymerase γ discriminates the four ribonucleotides differentially during DNA synthesis. The observed pattern is also dependent on the mitochondrial deoxyribonucleotide (dNTP) pools and disease-causing mutations that change these pools alter both the absolute and relative levels of incorporated ribonucleotides...
February 16, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28187197/genetic-variants-alter-t-bet-binding-and-gene-expression-in-mucosal-inflammatory-disease
#16
Katrina Soderquest, Arnulf Hertweck, Claudia Giambartolomei, Stephen Henderson, Rami Mohamed, Rimma Goldberg, Esperanza Perucha, Lude Franke, Javier Herrero, Vincent Plagnol, Richard G Jenner, Graham M Lord
The polarization of CD4+ T cells into distinct T helper cell lineages is essential for protective immunity against infection, but aberrant T cell polarization can cause autoimmunity. The transcription factor T-bet (TBX21) specifies the Th1 lineage and represses alternative T cell fates. Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) that may be causative for autoimmune diseases. The majority of these polymorphisms are located within non-coding distal regulatory elements...
February 10, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28187187/widespread-signatures-of-positive-selection-in-common-risk-alleles-associated-to-autism-spectrum-disorder
#17
Renato Polimanti, Joel Gelernter
The human brain is the outcome of innumerable evolutionary processes; the systems genetics of psychiatric disorders could bear their signatures. On this basis, we analyzed five psychiatric disorders, attention deficit hyperactivity disorder, autism spectrum disorder (ASD), bipolar disorder, major depressive disorder, and schizophrenia (SCZ), using GWAS summary statistics from the Psychiatric Genomics Consortium. Machine learning-derived scores were used to investigate two natural-selection scenarios: complete selection (loci where a selected allele reached fixation) and incomplete selection (loci where a selected allele has not yet reached fixation)...
February 10, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28187132/gwas-for-serum-galactose-deficient-iga1-implicates-critical-genes-of-the-o-glycosylation-pathway
#18
Krzysztof Kiryluk, Yifu Li, Zina Moldoveanu, Hitoshi Suzuki, Colin Reily, Ping Hou, Jingyuan Xie, Nikol Mladkova, Sindhuri Prakash, Clara Fischman, Samantha Shapiro, Robert A LeDesma, Drew Bradbury, Iuliana Ionita-Laza, Frank Eitner, Thomas Rauen, Nicolas Maillard, Francois Berthoux, Jürgen Floege, Nan Chen, Hong Zhang, Francesco Scolari, Robert J Wyatt, Bruce A Julian, Ali G Gharavi, Jan Novak
Aberrant O-glycosylation of serum immunoglobulin A1 (IgA1) represents a heritable pathogenic defect in IgA nephropathy, the most common form of glomerulonephritis worldwide, but specific genetic factors involved in its determination are not known. We performed a quantitative GWAS for serum levels of galactose-deficient IgA1 (Gd-IgA1) in 2,633 subjects of European and East Asian ancestry and discovered two genome-wide significant loci, in C1GALT1 (rs13226913, P = 3.2 x 10-11) and C1GALT1C1 (rs5910940, P = 2...
February 10, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28182654/elli-1-a-novel-germline-protein-modulates-rnai-activity-and-p-granule-accumulation-in-caenorhabditis-elegans
#19
Karolina M Andralojc, Anne C Campbell, Ashley L Kelly, Markus Terrey, Paige C Tanner, Ian M Gans, Michael J Senter-Zapata, Eraj S Khokhar, Dustin L Updike
Germ cells contain non-membrane bound cytoplasmic organelles that help maintain germline integrity. In C. elegans they are called P granules; without them, the germline undergoes partial masculinization and aberrant differentiation. One key P-granule component is the Argonaute CSR-1, a small-RNA binding protein that antagonizes accumulation of sperm-specific transcripts in developing oocytes and fine-tunes expression of proteins critical to early embryogenesis. Loss of CSR-1 complex components results in a very specific, enlarged P-granule phenotype...
February 9, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28182653/protecting-cells-by-protecting-their-vulnerable-lysosomes-identification-of-a-new-mechanism-for-preserving-lysosomal-functional-integrity-upon-oxidative-stress
#20
Raquel Pascua-Maestro, Sergio Diez-Hermano, Concepción Lillo, Maria D Ganfornina, Diego Sanchez
Environmental insults such as oxidative stress can damage cell membranes. Lysosomes are particularly sensitive to membrane permeabilization since their function depends on intraluminal acidic pH and requires stable membrane-dependent proton gradients. Among the catalog of oxidative stress-responsive genes is the Lipocalin Apolipoprotein D (ApoD), an extracellular lipid binding protein endowed with antioxidant capacity. Within the nervous system, cell types in the defense frontline, such as astrocytes, secrete ApoD to help neurons cope with the challenge...
February 9, 2017: PLoS Genetics
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